Package Clustalw

Code for calling ClustalW and parsing its output (DEPRECATED).
This module has been superseded by the Bio.AlignIO framework for
alignment parsing, and the ClustalW command line wrapper in
Bio.Align.Applications for calling the tool. These are both described
in the current version of the Biopython Tutorial and Cookbook.
This means Bio.Clustalw is now deprecated and likely to be
removed in future releases of Biopython.
A set of classes to interact with the multiple alignment command
line program clustalw.
Clustalw is the command line version of the graphical Clustalx
aligment program.
This requires clustalw available from:
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/.
functions:
o read
o parse_file
o do_alignment
classes:
o ClustalAlignment
o MultipleAlignCL

do_alignment(command_line,
alphabet=None)

Perform an alignment with the given command line (OBSOLETE).
Arguments:
o command_line - A command line object that can give out
the command line we will input into clustalw.
o alphabet - the alphabet to use in the created alignment. If not
specified IUPAC.unambiguous_dna and IUPAC.protein will be used for
dna and protein alignment respectively.
Returns:
o A clustal alignment object corresponding to the created alignment.
If the alignment type was not a clustal object, None is returned.
This function (and the associated command line object) are now obsolete.
Please use the Bio.Align.Applications.ClustalwCommandline wrapper with
the Python subprocess module (and Bio.AlignIO for parsing) as described
in the tutorial.

__warningregistry__

Value:

{('Bio.Clustalw is deprecated. Please use the Bio.AlignIO framework for alignment parsing, and the ClustalW command line wrapper in Bio.Align.Applications for calling the tool. These are both described in the current version of the Biopython Tutorial and Cookbook.',
<class 'Bio.BiopythonDeprecationWarning'>,
34): 1,('This class is obsolete.',
<type 'exceptions.PendingDeprecationWarning'>,...